Jetstream: Fails RNA-STAR 2.7.5b

[jennaj]

Galaxy Tool ID: toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.5b

Test history. Includes both mouse and human genome targets. hg19 failed -- and it was thought to have CVMFS indexes correct for this tool already (mouse not yet). Maybe some other problem?

• NEW (clean): https://usegalaxy.org/u/jen-galaxyproject/h/test-history-rnastar
• LAST WEEK (messy): https://usegalaxy.org/u/jen-galaxyproject/h/test-mappers-and-clusters-tests-rna-human

Example error: data 13-15 (individual paired-end RNA-seq reads, no GTF, target genome hg19)

slurmstepd: error: couldn't chdir to `/srv/pulsar/main/venv/lib/python3.6/site-packages': No such file or directory: going to /tmp instead

EXITING because of FATAL ERROR: could not open genome file /cvmfs/data.galaxyproject.org/managed/rnastar/2.7.4a/hg19/hg19/dataset_e434ec00-2efb-4ecd-bf63-878223a9c4d4_files//genomeParameters.txt
SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permsissions

Sep 14 20:42:03 ...... FATAL ERROR, exiting
[E::hts_open_format] Failed to open file "/jetstream/scratch0/main/jobs/30602736/outputs/dataset_45122796.dat" : No such file or directory
[E::hts_open_format] Failed to open file "/jetstream/scratch0/main/jobs/30602736/outputs/dataset_45122796.dat" : No such file or directory

Reported in bug reports and at Galaxy Help: https://help.galaxyproject.org/t/another-star-error/4442

cc @natefoo @davebx

[jennaj]

Priority genomes as part of #292 (closed) and #266 (current)

hg38
hg19
mm10
mm9
rn6
dm6
dm3
ce10

[jennaj]

"9/14/20 Tests" status

9/15/20 noon

1. hg38 -- success! individual inputs or collection -- this index is correct (expected)
2. hg19 -- fails all -- this index is not corrected yet or at least not when accessed from jetstream (unexpected)
3. mm9 -- fails individual inputs (collection queued) -- this index (and mm10) are pending the known correction (expected)

[jennaj]

Tool restricted to hg38 -- the only currently active working index for this tool version.

[jennaj]

More genomes indexed and working.
More will be added.
As those become available, each will appear on the tool form.